The multi-dimensional potential energy surface (PES) of a nanoparticle, such as a bare cluster of metal atoms, controls both the structure and dynamic behaviour of the particle. These properties are the subject of numerous theoretical simulations. However, quantitative experimental measurements of critical PES parameters are needed to regulate the models employed in the theoretical work. Experimental measurements of parameters are currently few in number, while model parameters taken from bulk systems may not be suitable for nanosystems. Here we describe a new measurement methodology, in which the isomer structures of a single deposited nanocluster are obtained frame-by-frame in an aberration-corrected scanning transmission electron microscope (ac-STEM) in high angle annular dark field (HAADF) mode. Several gold clusters containing 309 ± 15 atoms were analysed individually after deposition from a mass-selected cluster source onto an amorphous carbon film. The main isomers identified are icosahedral (Ih), decahedral (Dh) and face-centred-cubic (fcc) (the bulk structure), alongside many amorphous (glassy) structures. The results, which are broadly consistent with static ac-STEM measurements of an ensemble of such clusters, open the way to dynamic measurements of many different nanoparticles of diverse sizes, shapes and compositions.